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In the case of *dependencies* that get refreshed, no they're *not* kept in sys.modules - they get overwritten by the originals when the sys.modules state gets restored.
The problem almost certainly arises because something, somewhere is doing "from x import y", where y is a function that depends on module globals in 'x'.
If 'x' ever drops out of sys.modules (e.g. because it is a fresh copy only there temporarily during an import), the x.__dict__ will have every attribute set to None and calls to 'y' will fail. (In Florent's original example, it was his "dummy/foo.py" that set of alarm bells and prompted me to look up the reference for the module GC problem).
That's why I'm opposed to touching import_fresh_modules to sweep this problem under the rug - as long as module globals finalisation isn't GC based, keeping a reference to a function in a module without ensuring you also hold a reference to the module itself is always going to be somewhat dubious.